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CHECK report for bigmelon on merida2

This page was generated on 2019-04-09 13:33:58 -0400 (Tue, 09 Apr 2019).

Package 132/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bigmelon 1.9.0
Tyler J. Gorrie-Stone
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/bigmelon
Branch: master
Last Commit: 8a24a4c
Last Changed Date: 2018-10-30 11:54:36 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: bigmelon
Version: 1.9.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:bigmelon.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings bigmelon_1.9.0.tar.gz
StartedAt: 2019-04-08 23:27:41 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 23:34:53 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 432.2 seconds
RetCode: 0
Status:  OK 
CheckDir: bigmelon.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:bigmelon.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings bigmelon_1.9.0.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/bigmelon.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bigmelon/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bigmelon’ version ‘1.9.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘bigmelon’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘BiocGenerics’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘bumphunter:::greaterOrEqual’ ‘minfi:::pickCompProbes’
  ‘minfi:::projectCellType’ ‘wateRmelon:::.impose’
  ‘wateRmelon:::.normalizeQuantiles2’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  prcomp.gds.class
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bumphunterEngine.gdsn: no visible binding for global variable
  ‘locfitByCluster’
bumphunterEngine.gdsn: no visible global function definition for
  ‘getDoParRegistered’
bumphunterEngine.gdsn: no visible global function definition for
  ‘registerDoSEQ’
bumphunterEngine.gdsn: no visible global function definition for
  ‘getDoParWorkers’
bumphunterEngine.gdsn: no visible global function definition for
  ‘getDoParName’
bumphunterEngine.gdsn: no visible global function definition for
  ‘getDoParVersion’
bumphunterEngine.gdsn: no visible global function definition for
  ‘smoother’
bumphunterEngine.gdsn: no visible global function definition for
  ‘regionFinder’
bumphunterEngine.gdsn: no visible global function definition for
  ‘%dorng%’
bumphunterEngine.gdsn: no visible global function definition for
  ‘foreach’
bumphunterEngine.gdsn: no visible global function definition for ‘iter’
bumphunterEngine.gdsn: no visible binding for global variable
  ‘regionFinder’
bumphunterEngine.gdsn : computation.tots: no visible global function
  definition for ‘%dorng%’
bumphunterEngine.gdsn : computation.tots: no visible global function
  definition for ‘foreach’
bumphunterEngine.gdsn : computation.tots: no visible global function
  definition for ‘iter’
bumphunterEngine.gdsn : computation.tots2: no visible global function
  definition for ‘%dorng%’
bumphunterEngine.gdsn : computation.tots2: no visible global function
  definition for ‘foreach’
bumphunterEngine.gdsn : computation.tots2: no visible global function
  definition for ‘iter’
es2gds: no visible global function definition for ‘colData’
estimateCellCounts.gds: no visible global function definition for
  ‘colData’
Undefined global functions or variables:
  %dorng% colData foreach getDoParName getDoParRegistered
  getDoParVersion getDoParWorkers iter locfitByCluster regionFinder
  registerDoSEQ smoother
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
       user system elapsed
iadd 35.201   1.79  37.287
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/bigmelon.Rcheck/00check.log’
for details.



Installation output

bigmelon.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL bigmelon
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘bigmelon’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘fot’ in package ‘bigmelon’
Creating a new generic function for ‘predictSex’ in package ‘bigmelon’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (bigmelon)

Tests output

bigmelon.Rcheck/tests/runTests.Rout


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("bigmelon")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA


Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid



Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum


Attaching package: 'Biostrings'

The following object is masked from 'package:DelayedArray':

    type

The following object is masked from 'package:base':

    strsplit

locfit 1.5-9.1 	 2013-03-22
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

Attaching package: 'lumi'

The following objects are masked from 'package:methylumi':

    estimateM, getHistory


Attaching package: 'bigmelon'

The following objects are masked from 'package:wateRmelon':

    fot, predictSex

t8.gds doesn't exist, creating new file
creating gdsfile...
betas... 
pvals... 
methylated... 
unmethylated... 
fData... 
pData... 
qcdata... 
finished creating gdsfile
Directing 'rownames' to fData/TargetID by default, change with redirect.gds if incorrect.
Directing 'colnames' to pData/sampleID by default, change with redirect.gds if incorrect.
t9.gds doesn't exist, creating new file
creating gdsfile...
betas... 
pvals... 
methylated... 
unmethylated... 
fData... 
pData... 
qcdata... 
finished creating gdsfile
Directing 'rownames' to fData/TargetID by default, change with redirect.gds if incorrect.
Directing 'colnames' to pData/sampleID by default, change with redirect.gds if incorrect.
t2.gds doesn't exist, creating new file
creating gdsfile...
betas... 
pvals... 
methylated... 
unmethylated... 
fData... 
pData... 
qcdata... 
finished creating gdsfile
Directing 'rownames' to fData/TargetID by default, change with redirect.gds if incorrect.
Directing 'colnames' to pData/sampleID by default, change with redirect.gds if incorrect.
appending to /Users/biocbuild/bbs-3.9-bioc/meat/bigmelon.Rcheck/tests/t2.gds
betas... 
pvals... 
methylated... 
unmethylated... 
fData... 
pData... 
qcdata... 
t3.gds doesn't exist, creating new file
creating gdsfile...
betas... 
pvals... 
methylated... 
unmethylated... 
fData... 
pData... 
qcdata... 
finished creating gdsfile
Directing 'rownames' to fData/TargetID by default, change with redirect.gds if incorrect.
Directing 'colnames' to pData/sampleID by default, change with redirect.gds if incorrect.
t4.gds doesn't exist, creating new file
creating gdsfile...
betas... 
pvals... 
methylated... 
unmethylated... 
fData... 
pData... 
qcdata... 
finished creating gdsfile
Directing 'rownames' to fData/TargetID by default, change with redirect.gds if incorrect.
Directing 'colnames' to pData/sampleID by default, change with redirect.gds if incorrect.
t0.gds doesn't exist, creating new file
creating gdsfile...
betas... 
pvals... 
methylated... 
unmethylated... 
fData... 
pData... 
qcdata... 
finished creating gdsfile
Directing 'rownames' to fData/TargetID by default, change with redirect.gds if incorrect.
Directing 'colnames' to pData/sampleID by default, change with redirect.gds if incorrect.
t5.gds doesn't exist, creating new file
creating gdsfile...
betas... 
pvals... 
methylated... 
unmethylated... 
fData... 
pData... 
qcdata... 
finished creating gdsfile
Directing 'rownames' to fData/TargetID by default, change with redirect.gds if incorrect.
Directing 'colnames' to pData/sampleID by default, change with redirect.gds if incorrect.
t7.gds doesn't exist, creating new file
creating gdsfile...
betas... 
pvals... 
methylated... 
unmethylated... 
fData... 
pData... 
qcdata... 
finished creating gdsfile
Directing 'rownames' to fData/TargetID by default, change with redirect.gds if incorrect.
Directing 'colnames' to pData/sampleID by default, change with redirect.gds if incorrect.
t6.gds doesn't exist, creating new file
creating gdsfile...
betas... 
pvals... 
methylated... 
unmethylated... 
fData... 
pData... 
qcdata... 
finished creating gdsfile
Directing 'rownames' to fData/TargetID by default, change with redirect.gds if incorrect.
Directing 'colnames' to pData/sampleID by default, change with redirect.gds if incorrect.


RUNIT TEST PROTOCOL -- Mon Apr  8 23:34:41 2019 
*********************************************** 
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
bigmelon RUnit Tests - 8 test functions, 0 errors, 0 failures
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 
> 
> 
> proc.time()
   user  system elapsed 
 17.788   0.949  18.833 

Example timings

bigmelon.Rcheck/bigmelon-Ex.timings

nameusersystemelapsed
GEOtoGDS000
app2gds0.6450.0490.697
backupGdsn0.1930.0170.213
bigmelon-accessors3.1400.8374.058
bigmelon-internal0.1980.0190.222
bigmelon-normalization2.6820.3433.585
combogds0.5640.0470.649
es2gds0.3010.0250.331
finalreport2gds0.0000.0000.001
gds2mlumi0.6920.0500.750
getquantilesandranks0.4380.0370.487
iadd35.201 1.79037.287
pfiltergds0.4340.0330.476
prcompgdsn0.2330.0230.259
pwodgdsn0.6180.0400.666
rankednorm0.2410.0290.277
redirect0.2540.0310.289